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Bugfix/kbdev 1115 get cancer genes #104

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merged 5 commits into from
Oct 26, 2023

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mathieulemieux
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As per DEVSU-2032/DEVSU-2038 requirements.

Following datafix KBDEV-1084.

  • Add a get_cancer_genes() function to retreive list of all unique genes with a 'cancer gene' statement.
  • Refeactor get_oncokb_gene_list() into get_tumourigenesis_genes_list() allowing for a more generic usage

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codecov bot commented Oct 24, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (665b82a) 91.97% compared to head (5558922) 90.33%.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #104      +/-   ##
==========================================
- Coverage   91.97%   90.33%   -1.65%     
==========================================
  Files           8        8              
  Lines         835      838       +3     
==========================================
- Hits          768      757      -11     
- Misses         67       81      +14     
Flag Coverage Δ
unittests 90.33% <100.00%> (-1.65%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
graphkb/constants.py 93.61% <100.00%> (+0.28%) ⬆️
graphkb/genes.py 92.57% <100.00%> (+0.04%) ⬆️

... and 1 file with indirect coverage changes

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sshugsc
sshugsc previously approved these changes Oct 24, 2023
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looks good to me. would be better to write a test for get_cancer_genes()

sshugsc
sshugsc previously approved these changes Oct 24, 2023
elewis2
elewis2 previously approved these changes Oct 26, 2023
@mathieulemieux mathieulemieux changed the base branch from master to develop October 26, 2023 17:32
@mathieulemieux mathieulemieux dismissed stale reviews from elewis2 and sshugsc October 26, 2023 17:32

The base branch was changed.

@mathieulemieux mathieulemieux merged commit ad3baf3 into develop Oct 26, 2023
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3 participants